There is considerable evidence for the application of transplantation of Hematopoietic and Mesenchymal Stem Cells in the treatment of a wide range of cancers including lymphoma, neuroblastoma, and multiple myeloma. In addition, HSC/MSC therapies can be applied to reconstitute the immune system, regenerate damaged tissues, and deliver genes to repair damaged cells for many auto-immune diseases such as diabetes, rheumatoid arthritis, and system lupus erythematosis. One of the major roadblocks in the successful application of transplant treatments is the difficulty in obtaining a pure sample of stem cells in the harvested sample. This results in reinfusion of a larger number of residual tumor cells into the patient than is desirable, resulting, in some cases, in relapse of the disease. The ability to acquire a pure stem cell sample is therefore highly desirable. This research is focussed specifically on the development of a high-purity cell sorted for stem cell harvesting. The cell sorter uses a hierarchical multistage strategy with each sorting stage operating on the results of the previous sort thus reintorraging a sorted sample to verify its accuracy. The overall objective of this research is a sorter that results in a sample with greater than 99.9% purity through the use of multiple sorts.